Added 2FAST2Q module

modules/nf-core/fast2q/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fast2q=2.7.2

modules/nf-core/fast2q/main.nf

@@ -0,0 +1,38 @@
+process FAST2Q {
+
+    tag "2FAST2Q"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fast2q' :
+        'biocontainers/2.7.2--pyh7e72e81_0' }"
+
+    input:
+    tuple val(meta1), path(fastq)
+    tuple val(meta2), path(library)
+
+    output:
+    tuple val(meta), path("./2FAST2Q_output/*.*")   , emit: processed
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args            = task.ext.args ?: ''
+    def input_file      = "--s ${fastq}" ?: ''
+    def library_file    = (library instanceof Path && library.exists()) ? "--g ${library}" : ''
+
+    """
+    mkdir -p ./2FAST2Q_output
+
+    2fast2q -c --o ./2FAST2Q_output/ $input_file $library_file $args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${task.process}:
+        python: \$(python --version | sed 's/Python //g')
+        2FAST2Q version: \$(2fast2q -v | grep 'Version:' | sed 's/Version: //g')
+    END_VERSIONS
+    """
+}

modules/nf-core/fast2q/meta.yml

@@ -0,0 +1,63 @@
+name: fast2q
+description: A program that counts sequence occurrences in FASTQ files.
+keywords:
+- CRISPRi
+- FASTQ
+- genomics
+tools:
+- 2FAST2Q:
+    description: |
+      2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments.
+      2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences.
+      2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences.
+    homepage: https://github.com/afombravo/2FAST2Q
+    doi: 10.7717/peerj.14041
+    licence: ["GPL-3.0-or-later"]
+    identifier: ''
+
+input:
+- - meta1:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: FASTQ file
+      pattern: "*.{fastq,gz}"
+
+- - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - library:
+      type: file
+      description: library file
+      pattern: "*.csv"
+
+output:
+- processed:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:true ]
+      pattern: "./2FAST2Q_output/*.*"
+
+  - ./2FAST2Q_output/*.*:
+      type: map
+      description: |
+        Folder containing all the processed data
+      pattern: "./2FAST2Q_output/*.*"
+
+- versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+- "@afombravo"
+maintainers:
+- "@afombravo"

modules/nf-core/fast2q/tests/main.nf.test

@@ -0,0 +1,104 @@
+nextflow_process {
+
+    name "Test Process 2FAST2Q"
+    script "../main.nf"
+    process "FAST2Q"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fast2q"
+
+    config './nextflow.config'
+
+    test("Extracting all features at position=0 with default length of 20bp from a FASTQ file (without optional library.csv)") {
+
+        when {
+
+            params {
+                module_args = '--mo EC'
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test1', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + '/SRR8983579.small.fastq.gz', checkIfExists: true) // FASTQ file
+                ]
+                input[1] = [
+                    [ id:'test2', single_end:true ], // meta map for second input
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.processed).exists() } // Check processed output exists
+                { assert path(process.out.versions).readLines().join("\n").contains("2FAST2Q version") } // Verify version output
+            )
+        }
+
+    }
+
+    test("2FAST2Q self-test") {
+
+        when {
+
+            params {
+            module_args = '-t'
+                }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test1', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + '/SRR8983579.small.fastq.gz', checkIfExists: true) // FASTQ file
+                ]
+                input[1] = [
+                    [ id:'test2', single_end:true ], // meta map for second input
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.processed).exists() } // Check processed output exists
+                { assert path(process.out.versions).readLines().join("\n").contains("2FAST2Q version") } // Verify version output
+            )
+        }
+
+    }
+
+    /* test("FASTQ file with optional library") {
+
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test1', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + '/SRR8983579.small.fastq.gz', checkIfExists: true) // FASTQ file
+                ]
+                input[1] = [
+                    [ id:'test2', single_end:true ], // meta map for second input
+                    file(params.modules_testdata_base_path + '/D39V_guides.csv', checkIfExists: true) // library file
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.processed).exists() } // Check processed output exists
+                { assert path(process.out.versions).readLines().join("\n").contains("2FAST2Q version") } // Verify version output
+            )
+        }
+    } */
+
+}

modules/nf-core/fast2q/tests/nextflow.config

@@ -0,0 +1,10 @@
+params {
+    modules_testdata_base_path = "https://github.com/nf-core/test-datasets/tree/crisprseq/testdata"
+    module_args = '' // Default to an empty string
+}
+
+process {
+  withName: 'FAST2Q' {
+    ext.args = params.module_args
+  }
+}

modules/nf-core/fast2q/tests/tags.yml

@@ -0,0 +1,2 @@
+fast2q:
+  - "modules/nf-core/fast2q/**"